Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

Metatranscriptomic Analysis of Arctic Peat Soil Microbiota

(2014) Alexander T. Tveit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback

(2014) Martina Štursová et al.   ISME Journal

Land Use Type Significantly Affects Microbial Gene Transcription in Soil

(2014) Heiko Nacke et al.   MICROBIAL ECOLOGY

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling

(2014) Carolyn Churchland et al.   Frontiers in Microbiology

Metatranscriptomic Analyses of Plankton Communities Inhabiting Surface and Subpycnocline Waters of the Chesapeake Bay during Oxic-Anoxic-Oxic Transitions

(2013) Ian Hewson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED

(2013) Tomáš Větrovský et al.   BIOLOGY AND FERTILITY OF SOILS

Tree species influence on microbial communities in litter and soil: Current knowledge and research needs

(2013) Cindy E. Prescott et al.   FOREST ECOLOGY AND MANAGEMENT

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters

(2013) James T Hollibaugh et al.   ISME Journal

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Seasonal dynamics of fungal communities in a temperate oak forest soil

(2013) Jana Voříšková et al.   NEW PHYTOLOGIST

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling

(2013) A. Ekblad et al.   PLANT AND SOIL

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Discovery of Glycoside Hydrolase Enzymes in an Avicel-Adapted Forest Soil Fungal Community by a Metatranscriptomic Approach

(2013) Kazuto Takasaki et al.   PLoS One

Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation

(2013) Stéphane Uroz et al.   PLoS One

Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest

(2013) K. E. Clemmensen et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing

(2012) Melanie Kuffner et al.   FEMS MICROBIOLOGY ECOLOGY

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers

(2012) Martina Štursová et al.   FEMS MICROBIOLOGY ECOLOGY

Expression patterns reveal niche diversification in a marine microbial assemblage

(2012) Scott M Gifford et al.   ISME Journal

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

(2012) Alexander Tveit et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Responses of the extracellular enzyme activities in hardwood forest to soil temperature and seasonality and the potential effects of climate change

(2012) Petr Baldrian et al.   SOIL BIOLOGY & BIOCHEMISTRY

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR

(2011) Nicolas Chemidlin Prévost-Bouré et al.   PLoS One

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

(2010) R. Henrik Nilsson et al.   Fungal Ecology

Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi

(2010) Björn D Lindahl et al.   ISME Journal

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil

(2010) Christina Kaiser et al.   NEW PHYTOLOGIST

Quantification of effects of season and nitrogen supply on tree below-ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest

(2010) Mona N. Högberg et al.   NEW PHYTOLOGIST

Effects of soil properties and management on the activity of soil organic matter transforming enzymes and the quantification of soil-bound and free activity

(2010) Martina Štursová et al.   PLANT AND SOIL

Using Deep RNA Sequencing for the Structural Annotation of the Laccaria Bicolor Mycorrhizal Transcriptome

(2010) Peter E. Larsen et al.   PLoS One

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics

(2008) M. Sagova-Mareckova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil

(2008) Jaroslav Šnajdr et al.   SOIL BIOLOGY & BIOCHEMISTRY